Bob4's reply reminded me of something that may or may not be a factor. With that Yamaha, if you were in stereo mode and had the M50s set "large", all the main channel bass would go to the M50s and none to the sub unless you set the sub "both". In general, put the sub in the tightest corner behind the M50s, set all speakers "small", and set subwoofer only, not "both". Since the receiver is then handling the crossover at 90Hz, the crossover in the sub is just interfering, so turn it all the way up to get it as far out of the way as possible.
